featurecounts-rna-counting

What problem does it solve?

This Skill automates the process of counting RNA sequencing reads that overlap with specific genomic features, such as genes, from aligned sequencing data.

Core Features & Use Cases

• Gene-level Quantification: Generates a count matrix essential for differential gene expression analysis.
• Multi-sample Processing: Efficiently handles multiple BAM files in a single run.
• Strandedness Handling: Correctly accounts for library preparation protocols (unstranded, stranded, reverse-stranded).
• Use Case: After aligning RNA-seq reads to a reference genome, use this Skill to count how many reads map to each gene across all your experimental samples, preparing the data for tools like DESeq2 or edgeR.

Quick Start

Run featureCounts to count RNA-seq reads from multiple BAM files using the provided GTF annotation file and save the output to 'gene_counts.txt'.